[2023-06-08 11:46:55,215] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:46:55,218] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:46:55,219] [INFO] DQC Reference Directory: /var/lib/cwl/stg886f31a9-d5c3-4109-bfb6-ff32c1011e08/dqc_reference
[2023-06-08 11:46:56,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:46:56,569] [INFO] Task started: Prodigal
[2023-06-08 11:46:56,570] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ad52a37-7329-4145-85b6-7e18c23926ae/GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:47:02,342] [INFO] Task succeeded: Prodigal
[2023-06-08 11:47:02,343] [INFO] Task started: HMMsearch
[2023-06-08 11:47:02,343] [INFO] Running command: hmmsearch --tblout GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg886f31a9-d5c3-4109-bfb6-ff32c1011e08/dqc_reference/reference_markers.hmm GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:47:02,601] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:47:02,602] [INFO] Found 6/6 markers.
[2023-06-08 11:47:02,629] [INFO] Query marker FASTA was written to GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:47:02,630] [INFO] Task started: Blastn
[2023-06-08 11:47:02,630] [INFO] Running command: blastn -query GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg886f31a9-d5c3-4109-bfb6-ff32c1011e08/dqc_reference/reference_markers.fasta -out GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:47:03,263] [INFO] Task succeeded: Blastn
[2023-06-08 11:47:03,266] [INFO] Selected 12 target genomes.
[2023-06-08 11:47:03,267] [INFO] Target genome list was writen to GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:47:03,269] [INFO] Task started: fastANI
[2023-06-08 11:47:03,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ad52a37-7329-4145-85b6-7e18c23926ae/GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:47:09,765] [INFO] Task succeeded: fastANI
[2023-06-08 11:47:09,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg886f31a9-d5c3-4109-bfb6-ff32c1011e08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:47:09,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg886f31a9-d5c3-4109-bfb6-ff32c1011e08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:47:09,767] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:47:09,767] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:47:09,767] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-08 11:47:09,769] [INFO] DFAST Taxonomy check result was written to GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:47:09,770] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:47:09,770] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:47:09,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg886f31a9-d5c3-4109-bfb6-ff32c1011e08/dqc_reference/checkm_data
[2023-06-08 11:47:09,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:47:09,803] [INFO] Task started: CheckM
[2023-06-08 11:47:09,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:47:33,574] [INFO] Task succeeded: CheckM
[2023-06-08 11:47:33,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:47:33,597] [INFO] ===== Completeness check finished =====
[2023-06-08 11:47:33,597] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:47:33,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:47:33,598] [INFO] Task started: Blastn
[2023-06-08 11:47:33,598] [INFO] Running command: blastn -query GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg886f31a9-d5c3-4109-bfb6-ff32c1011e08/dqc_reference/reference_markers_gtdb.fasta -out GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:47:34,649] [INFO] Task succeeded: Blastn
[2023-06-08 11:47:34,654] [INFO] Selected 19 target genomes.
[2023-06-08 11:47:34,655] [INFO] Target genome list was writen to GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:47:34,663] [INFO] Task started: fastANI
[2023-06-08 11:47:34,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ad52a37-7329-4145-85b6-7e18c23926ae/GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:47:42,822] [INFO] Task succeeded: fastANI
[2023-06-08 11:47:42,836] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 11:47:42,836] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_014799385.1	s__CAG-115 sp014799385	91.7215	620	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799395.1	s__CAG-115 sp014799395	78.3373	219	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587465.1	s__CAG-115 sp910587465	78.1019	221	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555855.1	s__CAG-115 sp004555855	77.8835	153	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579125.1	s__CAG-115 sp910579125	77.7914	217	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017847835.1	s__CAG-115 sp017847835	77.7314	155	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554555.1	s__CAG-115 sp004554555	77.6231	158	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304735.1	s__CAG-115 sp002304735	77.6074	154	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003516865.1	s__CAG-115 sp003516865	77.3126	140	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.36	98.32	0.85	0.83	3	-
GCA_900542145.1	s__CAG-115 sp003507295	77.0921	85	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.16	97.02	0.91	0.87	5	-
GCA_003531585.1	s__CAG-115 sp003531585	76.848	74	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.38	98.23	0.90	0.86	9	-
GCA_004555635.1	s__CAG-115 sp004555635	76.8048	74	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.06	98.06	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-06-08 11:47:42,838] [INFO] GTDB search result was written to GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:47:42,839] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:47:42,841] [INFO] DFAST_QC result json was written to GCA_947175385.1_SRR14411333_bin.6_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:47:42,842] [INFO] DFAST_QC completed!
[2023-06-08 11:47:42,842] [INFO] Total running time: 0h0m48s